Directory Structure

To comply with both BIDS specification and Snakemake standard, the following directory structure has been adopted (with example intermediate workflows):

    results/  <-- list of derivative datasets
        fmriprep  
           dataset_description.json
              sub-01/
              sub-02/
        hippunfold 
            sub-01
            work

results

The top-level directory retains a single results folder containing all of the processed data. This results folder contains the final output (eg. necessary files) of the workflow and stores them according to the BIDS standard. To comply with the standard, a dataset_description.json file is also included in this results folder.

sourcedata

sourcedata contains the intermediate files generated to produce the final output. The directory is named to comply with the BIDS standard, while also being ignored by the BIDS validator. Each sub-directory within this directory is associated with a .smk file, with individual subject directories nested within the sub-directories.